[Bioperl-l] GenBank entries creation dates

Chris Fields cjfields at uiuc.edu
Mon Apr 7 11:46:01 EDT 2008


Strangely enough, if you use NCBI's esummary you can get both dates.   
Via Bio::DB::EUtilities in bioperl-live, if you dump out DocSum data  
(using a debugging method I added in a while back):

---------------------------------------

use Bio::DB::EUtilities;

# for multiple IDs use an array ref; also only use GI's (not accessions)
my $factory = Bio::DB::EUtilities->new(
                         -eutil => 'esummary',
                         -db => 'protein',
                         -id => 1621261);

$factory->print_DocSums;

---------------------------------------

One gets the following tag/value pairs:

UID: 1621261
Caption             :CAB02640
Title               :PROBABLE PYRIMIDINE OPERON REGULATORY PROTEIN  
PYRR [Mycobacterium tuberculosis
		     H37Rv]
Extra               :gi|1621261|emb|CAB02640.1|[1621261]
Gi                  :1621261
CreateDate          :2003/11/21
UpdateDate          :2006/11/14
Flags               :
TaxId               :83332
Length              :193
Status              :live
ReplacedBy          :
Comment             :

I'll add in a method to grab the data element by tag (in this case,  
grab the creation date by asking for the 'CreateDate' key).  Might  
come in handy for scripts.

chris

On Apr 7, 2008, at 7:48 AM, Heikki Lehvaslaiho wrote:

> Miguel,
>
> You probably know this but:
>
> - Your entry example below is a GenPept entry, not a GenBank entry
> - The NCBI sequence format "genbank" has only the last modified date.
>   I do not know about other formats (ASN.1, ...)
> - NCBI Entrez is a great tool but it obscures the source database.
> - If you really are working on real GenBank entries, you can use the  
> accession
> number to see find corresponding EMBL (and Swiss-Prot) flat file  
> formats that
> have both creation and last modified dates.
>
> Post to the list if you have trouble getting the dates from EMBL/ 
> Swiss-Prot
> formats using bioperl.
>
> Yours,
>
> 	-Heikki
>
> On Monday 07 April 2008 12:12:58 Miguel Pignatelli wrote:
>> Hi all,
>>
>> Is there any way to obtain the date of creation of individual GenBank
>> entries? I don't mean the "last revision" date that can be found in  
>> the
>> first line of a GenBank file.
>>
>> I can access this creation date by looking at the "revision  
>> history" of
>> any GenBank entry (for example, see
>> http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi? 
>> val=74311105),
>> but I need a systematic (and local=fast) way to access this  
>> information.
>>
>> Any help would be very appreciated,
>> Thank you very much in advance,
>>
>> M;
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> -- 
> ______ _/      _/_____________________________________________________
>      _/      _/
>     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
>    _/_/_/_/_/  Senior Scientist    skype: heikki_lehvaslaiho
>   _/  _/  _/  SANBI, South African National Bioinformatics Institute
>  _/  _/  _/  University of Western Cape, South Africa
>     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
> ___ _/_/_/_/_/________________________________________________________
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



More information about the Bioperl-l mailing list